A large number of useful substances are most efficiently produced by microorganisms such as bacteria or fungi (Shuler, M. L. and Kargi, R., Bioprocess Fundamientals (2nd Ed.), Prentice Hall (2001); Doran, P., Bioprocess Engineering Principles, Academic Press (1995)). This includes some pharmaceutical products, food additives and supplements, bulk chemicals such as ethanol, and enzymes. While organisms that produce the desired substance may occur in nature, their metabolism is likely not optimized to produce the desired product, and harvesting product from microorganisms as they exist in nature is frequently not practical. In addition, an increasing number of useful products including a variety of pharmaceutical agents (e.g., antibodies, enzymes) are produced by harvesting them from mammalian cells or culture medium. Bioprocess development typically involves improving the microorganism or cell (e.g., through selection, mutation, or recombinant DNA technology) and/or engineering its environment to produce the desired product with high efficiency.
Developing efficient and practical bioprocesses frequently involves testing a large number of different strains and environmental conditions in various combinations. Although the ultimate goal is to identify an appropriate strain and conditions for production on an industrial scale (e.g., in a bioreactor with a 100,000-300,000 liter volume), bioprocess development begins on a much smaller scale. For example, screening of different strains is often conducted in microtiter plates, under relatively uncontrolled conditions and with only limited possibility of monitoring conditions during culture. After identification of strains that appear promising, further screening is performed in shaking flasks with a much larger volume (e.g., 25-100 ml). Such flasks typically allow only partial control over important environmental variables and cannot achieve the high oxygen (O2) concentrations typically used in large-scale fermentation processes. Thus the usefulness of these open loop systems for selecting the organisms that will be optimal under actual bioprocess conditions is limited.
Scale-up to bench-scale, closed loop bioreactors, which offer improved control over environmental variables, increased oxygenation, and therefore the ability to achieve higher cell densities, is the next step. However, bench-scale bioreactors, with typical volumes of between 0.5 and 10 liters suffer from a number of drawbacks. Because of their large size, relatively high cost, and the time and effort required to obtain the data it is typically not practical to test as many combinations of strains and environmental conditions as would be desirable.
The inventors have recognized that there is a large technology gap between microtiter plates/flasks and closed loop controlled bioreactors. This gap is important because its presence may allow potentially productive strains to be eliminated at the microtiter plate or shake-flask screening stage, due to optimization with respect to uncontrolled physical parameters, or it may allow potentially non-productive strains that do not perform well under typical industrial scale bioprocess conditions, e.g., high cell densities, to proceed to the next stage. There is thus a need in the art for a system to fill this gap. In particular, there is a need for small scale bioreactor systems that allow multiple experiments to be performed in parallel without an accompanying increase in cost and that offer improved control over environmental parameters. However, in order to realize such a system, a number of challenges need to be overcome. One of these challenges is to develop a system that can provide effective mixing and oxygenation in a small volume.